No train stations near your destination? The route of the bus is difficult to understand? It is way too far to get there?
These are the cases when you might want to jump on a taxi. The driver will know her/his way around the area and you will be in safe hands. In Japan rip-offs are almost non-existent.
Once on the taxi, try to ask your driver if there are any places he/she recommends visiting and food that you should try when you get to your next destination. You might receive some precious piece of advice that you would have never found on a guidebook. Even if you don’t speak Japanese, you can say “Koko made onegai shimasu”, whilst pointing on the map on your destination and it will be enough to communicate where you are heading to.
The set price for a taxi drive varies from region to region, but it is usually about 1000 yen for 2 km of ride, to be rough. If you get a taxi between 10-11pm and 5am, an additional fee will be added.